d1ur3m_d1k87a1

Motif
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SCOPidRangeSCOP ClassSCOP FoldSCOP SuperfamilySCOP FamilyProtein
1ur3_Mh
d1ur3m_M215-M255,M263-M297Alpha and beta proteins (a/b)TIM beta/alpha-barrelNAD(P)-linked oxidoreductaseAldo-keto reductases (NADP)Hypothetical oxidoreductase YdhF
1k87_Ac
d1k87a1A138-A199,A200-A261All alpha proteinsN-terminal domain of bifunctional PutA proteinN-terminal domain of bifunctional PutA proteinN-terminal domain of bifunctional PutA proteinN-terminal domain of bifunctional PutA protein

Justification for analogy
The motif in 1ur3: helix 1 and 4 are insertions while helix 2 and 3 are TIM barrel helices. So this is a hybrid motif.


Alignment-based scores
AlignerAligned LengthSequence IdentityRMSDGDT-TSCOMPASS
manual570.087723.0282955.70175-10.40394
dali650.092314.1242349.61538-14.40383
tm420.095243.8358661.30952-15.98116
fast510.098044.2802838.72549-11.88813

In the alignments below, two upper-case letters are aligned, while two lower-case letters are NOT aligned. The two sequences in an alignment are NOT continuous in most cases (see their ranges). The superpositions are re-constructed from the corresponding alignments by minimizing the overall RMSD. In a PDB-format superposition file, the first domain is represented by chain S and the second domain is represented by chain A.

MANUAL alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1ur3_Mh   grlfnddYFQPLRDELAVVAEELNAgSIEQVVNAWVLRLPs---------------------------------------sgkieRVRAAVE-AETLk------mTRQQWFRIRKAALGydv-
1k87_Ac   -----qkNASGRAGMVQGLLQEFSL-SSQEGVALMCLAEAllripdkatrdalirdkisngnrspslfvnaatwgllftg-----NEASLSRsLNRIigksgeplIRKGVDMAMRLMGEqfvt

DALI alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1ur3_Mh   grlfnDDYFQPLRDELAVVAEELNAGSiEQVVNAWVLR--LPS-------------------S--------------gkiERVRAAVEAETLK------MTRQQWFRIRKAALGY-dv
1k87_Ac   -----QKNASGRAGMVQGLLQEFSLSS-QEGVALMCLAeaLLRipdkatrdalirdkisngnRspslfvnaatwgllftgNEASLSRSLNRIIgksgepLIRKGVDMAMRLMGEQfvt

TM alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1ur3_Mh   --------------GRL--FNDD-YFQPLRDELAVVAEEL-N---AGSIEQVVNAWVLRLPSSGKIERVRAAVEA----ETLKMTRQQWFRI------------RK-AAL--------------------------------GYDV
1k87_Ac   QKNASGRAGMVQGL--LQEFSLSSQEGVALMCLAEALLRIPDKATRDA-LI-------------------RDKISNGNR------S--PSLFVNAATWGLLFTGNEASLSRSLNRIIGKSGEPLIRKGVDMAMRLMGEQFVT----

FAST alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1ur3_Mh   GRLFNDDYF----QPLRDELAVVAEELNAGSIEQVVNAWVLRLPSSGK-------------------------------------------IERVRAAVEAETLKMT-----RQQWFRIRKAALGYDV---------
1k87_Ac   ---------QKNASGRAGMVQGLLQEFSLS-SQEGVALMCLAE-----ALLRIPDKATRDALIRDKISNGNRSPSLFVNAATWGLLFTGNEASLSRSLNRI------IGKSGEPLIRKGVDMAM----RLMGEQFVT